A Target Restricted Assembly Method (TRAM) for Phylogenomics

While next generation sequencing technology can produce sequences covering the entire genome, assembly and annotation are still prohibitive steps for many phylogenomics applications. Here we describe a method of Target Restricted Assembly (TRAM) of a single lane of Illumina sequences for genes of relevance to phylogeny reconstruction, i.e. single copy protein-coding genes. This method has the potential to produce a data set of hundreds of genes using only one Illumina lane per taxon

A semi-supervised approach to visualizing and manipulating overlapping communities

When evaluating a network topology, occasionally data structures cannot be segmented into absolute, heterogeneous groups. There may be a spectrum to the dataset that does not allow for this hard clustering approach and may need to segment using fuzzy/overlapping communities or cliques. Even to this degree, when group members can belong to multiple cliques, there leaves an ever present layer of doubt, noise, and outliers caused by the overlapping clustering algorithms. These imperfections can either be corrected by an expert user to enhance the clustering algorithm or to preserve their own mental models of the communities. Presented is a visualization that models overlapping community membership and provides an interactive interface to facilitate a quick and efficient means of both sorting through large network topologies and preserving the user's mental model of the structure. © 2013 IEEE

The 2005 AMI system for the transcription of speech in meetings

In this paper we describe the 2005 AMI system for the transcription\ud of speech in meetings used for participation in the 2005 NIST\ud RT evaluations. The system was designed for participation in the speech\ud to text part of the evaluations, in particular for transcription of speech\ud recorded with multiple distant microphones and independent headset\ud microphones. System performance was tested on both conference room\ud and lecture style meetings. Although input sources are processed using\ud different front-ends, the recognition process is based on a unified system\ud architecture. The system operates in multiple passes and makes use\ud of state of the art technologies such as discriminative training, vocal\ud tract length normalisation, heteroscedastic linear discriminant analysis,\ud speaker adaptation with maximum likelihood linear regression and minimum\ud word error rate decoding. In this paper we describe the system performance\ud on the official development and test sets for the NIST RT05s\ud evaluations. The system was jointly developed in less than 10 months\ud by a multi-site team and was shown to achieve very competitive performance